PMC

Multiple sequence alignment of bacterial Ku homologs. The first and last residue numbers are indicated before and after each sequence in the alignment. Positions corresponding to zinc-binding residues are boxed and marked by asterisks below the alignment. B_meg, Bacillus megaterium; B_ant, Bacillus anthracis; B_pum, Bacillus pumilus; B_sub, Bacillus subtilis; M_smg, Mycobacterium smegmatis; M_JLS, Mycobacterium Sp. JLS; M_KMS, Mycobacterium Sp. KMS; M_gil, Mycobacterium gilvum; M_van, Mycobacterium vanbaalenii; M_tub, Mycobacterium tuberculosis; M_bov, Mycobacterium bovis; M_mar, Mycobacterium marinum; M_ulc, Mycobacterium ulcerans; M_kan, Mycobacterium kansasii; M_avi, Mycobacterium avium; M_int, Mycobacterium intracellulare; S_coe, Streptomyces coelicolor; P_stu, Pseudomonas stutzeri; P_aeu, Pseudomonas aeruginosa; P_put, Pseudomonas putida.

Sequence alignment and secondary structure prediction of Lsr2 proteins in various actinomycetes. The alignment was produced using the CLUSTALW program. The secondary structure was analyzed by using the Jpred program (http://www.compbio.dundee.ac.uk/∼www-jpred/). The arrows represent β-strands and ovals represent α-helices. Species abbreviations: M. tb., Mycobacterium tuberculosis; M. marinum, Mycobacterium marinum; M. ulcerans, Mycobacterium ulcerans; M. avium, Mycobacterium avium; M. paratb, Mycobacterium avium subsp. paratuberculosis; M. leprae, Mycobacterium leprae; M. flavescens, Mycobacterium flavescens; M. gilvum, Mycobacterium gilvum; M. vanbaalenii, Mycobacterium vanbaalenii; M. smegmatis, Mycobacterium smegmatis; M. abscessus, Mycobacterium abscessus; N. farcinica, Nocardia farcinica; R. RHA1, Rhodococcus sp. strain RHA1; S. erythraea, Saccharopolyspora erythraea; S. avermitilis, Streptomyces avermitilis; S. coelicolor, Streptomyces coelicolor; S. griseus, Streptomyces griseus subsp. griseus; J. HTCC, Janibacter sp. strain HTCC2649; A. aurescens, Arthrobacter aurescens; R. salmoninarum, Renibacterium salmoninarum; F. alni, Frankia alni; M. luteus, Micrococcus luteus; Cjw1, Mycobacterium phage Cjw1; C. sepedonicus, Clavibacter michiganensis subsp. sepedonicus; K. rhizophila, Kocuria rhizophila; T. fusca, Thermobifida fusca; Omega, Mycobacterium phage Omega. The H-NS of E. coli is included in the alignment (bottom), but only the predicted secondary structure of Lsr2 is shown.

Mechanism of the binding of c-di-GMP to Ethr is general. (a). Sequence alignment and secondary structure element of Ethr in mycobacteria. Secondary structure element is showed above sequences. Sequence similarities are highlighted by black background (identities) and boxes (similarity). Red star represents conservative sites of Ethr with the binding of c-di-GMP at Q125, R181, E190. M.tb_H37Rv = Mycobacterium tuberculosis H37Rv, M.bovis = Mycobacterium bovis, M.tb_CDC1551 = Mycobacterium tuberculosii CDC1551, M.leprae = Mycobacterium leprae, M.marinum = Mycobacterium marinum, M.sm = Mycobacterium smegmatis. (b). Sequence alignment and secondary structure elements of TetR like protein in many strains. Sequence similarities are highlighted by black background (identities) and boxes (similarity). Helix α1, α2, and α3 with a higher conservation represent the DNA binding domain. M.tb = Mycobacterium tuberculosis, S.c = Streptomyces coelicolor, T.m = Thermotoga maritima. (c). Docking model of the four TetR like proteins with c-di-GMP. The affinity is showed above the model. Yellow boxes represent the pockets of protein that c-di-GMP binds to.

Sequence alignment of GMK homologs from Mycobacterium tuberculosis (Mtb), Streptomyces coelicolor and Bacillus subtilis. Yellow boxes indicate residues that interact with pppGpp and are conserved in all three species. Red boxes indicate residues that interact with pppGpp and are polymorphic in Mtb.